Variant report

Variant	rs57539299
Chromosome Location	chr18:9552639-9552640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr18:9552569-9553040	K562	blood:	n/a	n/a
2	CBX3	chr18:9552593-9553047	K562	blood:	n/a	n/a
3	KAP1	chr18:9552508-9552994	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9550057..9552721-chr18:9560835..9563453,2	K562	blood:

Variant related genes	Relation type
PPP4R1	TF binding region
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1036930	0.93[ASN][1000 genomes]
rs11081487	0.83[ASN][1000 genomes]
rs12327541	0.93[ASN][1000 genomes]
rs16955297	0.93[ASN][1000 genomes]
rs1869737	0.86[ASN][1000 genomes]
rs1869739	0.86[ASN][1000 genomes]
rs2028657	0.93[ASN][1000 genomes]
rs28365814	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2840354	1.00[ASN][1000 genomes]
rs3786174	0.90[ASN][1000 genomes]
rs55841197	0.93[ASN][1000 genomes]
rs56883068	0.93[ASN][1000 genomes]
rs58800301	0.86[ASN][1000 genomes]
rs58982927	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59114729	0.90[ASN][1000 genomes]
rs59992205	0.90[ASN][1000 genomes]
rs60290408	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61166388	0.90[ASN][1000 genomes]
rs61275183	0.86[ASN][1000 genomes]
rs62086114	0.83[ASN][1000 genomes]
rs62086115	0.83[ASN][1000 genomes]
rs62086118	0.83[ASN][1000 genomes]
rs62086119	0.83[ASN][1000 genomes]
rs62086120	0.83[ASN][1000 genomes]
rs62086121	0.83[ASN][1000 genomes]
rs62086146	0.90[ASN][1000 genomes]
rs62086147	0.90[ASN][1000 genomes]
rs62086151	0.90[ASN][1000 genomes]
rs62086152	0.90[ASN][1000 genomes]
rs62086155	0.90[ASN][1000 genomes]
rs62086156	0.90[ASN][1000 genomes]
rs62086158	0.90[ASN][1000 genomes]
rs62086159	0.90[ASN][1000 genomes]
rs62087363	0.90[ASN][1000 genomes]
rs62087368	0.90[ASN][1000 genomes]
rs62087370	0.90[ASN][1000 genomes]
rs62087371	0.90[ASN][1000 genomes]
rs62087372	0.84[ASN][1000 genomes]
rs62087378	0.90[ASN][1000 genomes]
rs62087402	0.90[ASN][1000 genomes]
rs62087403	0.90[ASN][1000 genomes]
rs62087404	0.90[ASN][1000 genomes]
rs62087406	0.90[ASN][1000 genomes]
rs62087407	0.90[ASN][1000 genomes]
rs62087411	0.90[ASN][1000 genomes]
rs62087412	0.90[ASN][1000 genomes]
rs62087414	0.90[ASN][1000 genomes]
rs62087415	0.90[ASN][1000 genomes]
rs62087416	0.90[ASN][1000 genomes]
rs62087417	0.86[ASN][1000 genomes]
rs62087427	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62087456	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62088860	0.93[ASN][1000 genomes]
rs62088870	0.93[ASN][1000 genomes]
rs62088872	0.93[ASN][1000 genomes]
rs62088873	0.93[ASN][1000 genomes]
rs62088875	0.93[ASN][1000 genomes]
rs62088876	0.93[ASN][1000 genomes]
rs62088880	0.86[ASN][1000 genomes]
rs62088881	0.86[ASN][1000 genomes]
rs62088884	0.86[ASN][1000 genomes]
rs62088885	0.86[ASN][1000 genomes]
rs62088904	0.86[ASN][1000 genomes]
rs62088906	0.86[ASN][1000 genomes]
rs62088908	0.81[ASN][1000 genomes]
rs6506677	0.93[ASN][1000 genomes]
rs7228280	0.81[ASN][1000 genomes]
rs7231531	0.86[ASN][1000 genomes]
rs7233308	0.93[ASN][1000 genomes]
rs7233649	0.86[ASN][1000 genomes]
rs7234355	0.93[ASN][1000 genomes]
rs7235935	0.86[ASN][1000 genomes]
rs7236274	0.86[ASN][1000 genomes]
rs7237018	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7238137	0.93[ASN][1000 genomes]
rs7239083	0.86[ASN][1000 genomes]
rs72636719	0.80[ASN][1000 genomes]
rs72945737	0.86[ASN][1000 genomes]
rs732698	0.86[ASN][1000 genomes]
rs73393877	0.83[ASN][1000 genomes]
rs73393880	0.90[ASN][1000 genomes]
rs73395717	0.90[ASN][1000 genomes]
rs73395719	0.90[ASN][1000 genomes]
rs8093600	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8096551	0.86[ASN][1000 genomes]
rs894757	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9535200-9556800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:9544000-9557000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr18:9544000-9570200	Strong transcription	Fetal Intestine Large	intestine
4	chr18:9544000-9575600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr18:9544200-9553200	Strong transcription	Thymus	Thymus
6	chr18:9544200-9563600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:9544400-9553800	Strong transcription	Spleen	Spleen
8	chr18:9544600-9561600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr18:9544600-9563600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr18:9544600-9563600	Strong transcription	Brain Cingulate Gyrus	brain
11	chr18:9544600-9564200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr18:9544600-9564200	Strong transcription	Placenta	Placenta
13	chr18:9544800-9552800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr18:9544800-9556800	Strong transcription	HMEC	breast
15	chr18:9544800-9557000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr18:9544800-9562000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr18:9544800-9564600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr18:9544800-9565000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr18:9544800-9572200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr18:9544800-9572400	Strong transcription	Primary T cells from cord blood	blood
21	chr18:9545000-9552800	Strong transcription	Primary hematopoietic stem cells	blood
22	chr18:9545000-9552800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr18:9545000-9554200	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr18:9545000-9557000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr18:9545000-9557200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr18:9545000-9562600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr18:9545000-9563800	Strong transcription	Osteobl	bone
28	chr18:9545000-9564200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr18:9545000-9564200	Strong transcription	Adipose Nuclei	Adipose
30	chr18:9545000-9564400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr18:9545200-9560400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr18:9545200-9561400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr18:9545200-9561600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr18:9545200-9563400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr18:9545200-9572600	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr18:9545400-9552800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:9545400-9560000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr18:9545400-9564000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr18:9545600-9554000	Strong transcription	NHLF	lung
40	chr18:9545800-9556200	Strong transcription	HepG2	liver
41	chr18:9545800-9563600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr18:9545800-9564200	Strong transcription	Fetal Thymus	thymus
43	chr18:9545800-9565000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr18:9545800-9570200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr18:9545800-9583600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr18:9545800-9595200	Strong transcription	Dnd41	blood
47	chr18:9546000-9555200	Strong transcription	Ovary	ovary
48	chr18:9546000-9557200	Strong transcription	NHEK	skin
49	chr18:9546000-9563800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr18:9546200-9552800	Strong transcription	Primary B cells from peripheral blood	blood

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